cheminformatics nomenclature activity binding based data sets knowledge thesauri article

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1 PubChem chemical biology domain caspase activity standards cheminformatics nomenclature activity semantic enzyme reporter viability fluorescence binding based data sets programming knowledge search screening technology end point thesauri article PDSP object enzyme substrate based XML versioning natural language high-thoughput screening (HTS) software classification Data Standards for Data Integration polysemes biological pathways Beta-Lactamase Induction specificity dehydrogenase activity GFP induction annotation properties subject indexing schemes Fluorogenic substrate Stephan Schürer chemical probes information exchange ChemBank ATP Luciferin Coupled servers classes University of Miami synonyms search tool biological assay controlled vocabulary biomedical knowledge disease networks SPARC Workshop, small molecule structure NIH, Feb meta-data concepts taxonomies subject headings calcium redistribution cyclic AMP redistribution RDF OWL novel chemical tools indexing library pharmaceutical semantic web authorized terms individuals structural biology tags homographs energy transfer

2 Types of data standards Reporting guideline (checklist) specifies what information need to be captured about an experiment for a particular purpose (Controlled) vocabulary terminological resource that provides the identification and definition of entities Data exchange format is a specification how data are encoded to be computer-readable / -processable Data structure refers to organization of data, data schema, entity relations 2

3 BioSharing Standards ( O. Search all of BloSharlng LOG IN OR REGISTER biosharing O<:> COMMUNITY CONTENT SUMMARY ABOUT Contribute by submitting a standard Found a bug? Please tell us! Standards BioSharing standards have been partly compiled by linking to BioPortal, MIBBI and the Equator Network. Or you can filter on MIBBI Foundry reporting guidelines or 080 Foundry terminology artifacts. arch for tandar O. Search MHHF ~Reset X REPORTING GUIDELINE View as Grid View as Table Showing records 1 50 of 69. D No Publlc1tlon [J Hl!IS Publication ~ No M1lnt1lner ~ Has M1lnulner Standard Type REPORTING GUIDELINE EXCHANGE FORMAT TERMINOLOGY ARTIFACT C'ear AMIS Article Minimum Information Standard ~Systems L.:., Publications REPORTING GUIOELINE a ARRIVE Animals in Research: Reporting In Vivo.. S Systems L.:., Publications REPORTING GUIOELINE a BioDBCore Core Attributes of Biological Databases ~Systems L.:., Publications REPORTING GUIOELINE a a 3

4 Checklists Minimum Information Guidelines a mibbi Bioscience reporting guidelines and Portal Minimum Information guidelines from diverse bioscience Foundry If you want to register your checklist to MIBBI, please contact the BioSharing team Excel spreadsheet and XML document (schema) describing all registered About Bioscience projects registered with MIBBI CIMR GIATE MIABE MIABiE Core Information for Metabolomics Reporting Guidelines for Information A bout Therapy Experiments Minimal Information About a Bioactive Entity Minimum Information About. a Biofilm Experiment I I!. x!. x MIACA MIAME MIAPA Minimal Information About a Cellular Assay Minimum Information About. a Microarray Experiment Minimum Information About a Phylogenetic Analysis I!. x MIAPAR Minimum Information About. a Protein Affinity Reagent MIAPE Minimum Information About a Proteomics Experiment MIAPegAE MIARE MIASE MIASPPE Minimum Information About. a Peptide Array Experiment Minimum Information About a RNAi Experiment Minimum Information About. a Simulation Experiment Minimum Information About Sample Preparation for a Phosphoproteomics Experiment I I!. x!. x MIATA Minimum Information About. T Cell Assays MICEE Minimum Information about a Cardiac Electrophysiology Experiment MIDE MIFlowCyj Minimum Information required for a DMET Experiment Minimum Information for a Flow Cytometry Experiment I!. x 4

5 Minimum Information Standard may not exist Regenbase: Integration of diverse data related to nerve regeneration in the context of spinal cord injury 5

6 Vocabulary vs. ontology Controlled vocabularies / thesauri describe what things mean (link terms to human description) Entities with identity criteria Share knowledge in a common language Natural language synonyms for search and text mining 6

7 Vocabulary vs. ontology Ontologies Contains entities (classes) and their relationships (object properties) Capture / abstract knowledge using logical axioms Explicit specification (OWL-DL) Building formal (computable) models Computing with knowledge (reasoning engines) Foundation of Semantic Web information systems 7

8 Ontology resources NCBO Bioportal EBI Ontology Lookup Service OLS OBO Foundry 8

9 Metadata specifications Metadata: Data not directly measured in an experiment (or obtained in a study) Why metadata: Facilitate data replicability, reproducibility, reuse Interpret results, perform data analysis, hypotheses Repurpose data for other projects Information systems (search, query, data integration and exchange) What metadata to capture in a standardized format with controlled vocabularies (and formal descriptions)? 9

10 A useful distinction of metadata Model metadata: Required to understand, interpret, and meaningfully integrate experimental results Typically queryable in software systems Important parameters to describe conclusions (data visualizations) Confounder metadata: Non model metadata required to replicate and reproduce experimental results Needed for data forensics (e.g. batches of reagents, maintenance of experimental equipment, etc.) 10

11 Standardized metadata Capture all (detailed descriptions, SOP) Make model metadata explicit (controlled vocabulary, standard format) But what s really model metadata? Data and informatics use cases Types of queries and analyses Integration with other data sources Information systems / UI components Consider re-use of data for other projects LINCS Metadata Standards: Vempati et al J Biomol Screen

12 Data Coordination V' '\/'l tw I Central Database I repository - Stch+flesulls+Nav ~ lfoav"j ID@ = ~ t:~ ~ Standards Computing Globalindex Data APls liiill! Repository I -~ "-t:~-repository 12

13 Data set IDs and provenance Permanent ID via (authoritaitve) repository or data publication DOI PURL Capture data provenance PROV-O: The PROV Ontology (W3C) PAV (Provenance, Authoring Versioning) Ontology 13

14 Provenance The link between source data, computation / processing and derived data / results static verifiable record track changes compare / discrepancies repeat / reproduce Citation version data release PDIFF, Woodman

15 RDBMS vs Semantic Web technologies RDBMS Closed world assumption No reasoning support Need to know schema for highly specialized queries Data sharing not easy, no semantics Efficient RDBMS access Established technology Industry standard Ontologies Open world assumption Reasoning support Provide restriction-free framework (formal semantics) Easy data/knowledge sharing Triple store access Relatively early stage Standards emerging

16 Replicability vs Reproducibility [repeat] same experiment same lab same experiment different set up [ rep1rod u ce] [replicate ] same experiment different lab different experiment some of same reuse Drummond C Replicabil ~ y is not Re oducibility: Nor is it Good Science, online Peng RD, Reproducible Research in Computational Science Science 2 Dec 2011: